Mega Man: Elf Wars
by Alagar3000
Summary: It is a time of healing. The death of Sigma has brought the maverick wars to an end and X works towards a cure for the virus, and to his vision of 'Elysium.' But it will not last, and his best friends return spells doom for the entire world.
1. Prologue

Elf Wars

Prologue

In a room filled with computers, sat a woman with long blond hair. On her desk were strewn about papers, each one containing various formulas and bits of coding. Some were circled, most were scratched out. She sighed as she brought a small metallic cylinder to her face and began to speak. "Entry for day five hundred and eighty two: I have just eliminated the forty seventh attempt as a viable candidate for a general purpose antibody. I'm down to the last six combinations, but my enthusiasm has dropped to an all time low. Out of the last dozen experiments, sample forty seven had had the highest simulated success rate when exposed to the virus. By all accounts, this should have been the breakthrough we were expecting. I just don't understand..."

"Uhm, excuse me, Doctor?" A voice intruded on her reverie.

She quickly looked up, startled that there was someone else in her lab. After a brief moment of shock, she recognized the figure who now stood at her door. A young looking man with black hair and piercing green eyes met her stare. He was holding a rather nondescript metal container in front of him and he seemed to be waiting for permission to enter her room. "Oh god, I'm sorry, you caught me off guard."

He looked slightly embarrassed. "I apologize. If this is a bad time, I can come back."

"No, no, this is fine. I just forgot you were coming in today. I'm sorry, I've had a lousy day. We just tried sample forty seven and it was a complete failure."

A look of concern came across his face. "Oh no! I'm really sorry to hear that. I suppose that means I'll have to keep on bringing you virus samples then?"

"Yeah, business as usual huh?"

He took a seat in an adjacent chair, on the other side of the doctor's desk. "Well, unfortunately, it is getting more difficult. The war, for all intents and purposes, is over and it's only a matter of time before we retire the last of the virus carriers, but who knows how long that will take. They've gotten smarter since Sigma's last death, almost as if the virus kept itself from turning them completely berserk. Hit and run is their main strategy now and by the time we get there, they've already left and we're stuck picking up the pieces. We're lucky if we can put one of them down, and even then getting a sample is a hazardous job in and of itself. There aren't many of my team who would willingly get that close to the virus."

The woman nodded as he talked, but then smiled. "That's why we're lucky you're the one leading the fight. You don't seem to have a problem getting close to the virus."

He let a bemused smile show on his face. "Well ma'am, that's because I don't fear it like they do. And that's what I tell my men every time we fight. We have to overcome our fear of what our enemy has, or else it will consume us. I lost a lot of friends to the virus, but I know it can be beat. Until then, however, I'll keep bringing you the samples you need along with any other assistance I can provide."

"Well, what I could really use is a fresh take on some of the coding I've been working on. I've looked over them too many times and Guntram is being his usual self."

"Ah, well…" He adopted a sheepish look on his face as he rubbed the back of his head. "I'm not much for computer code ma'am. That was my father's area, and I can't hope to be what he was at his height. "

The woman sighed as she leaned back in her chair. "I suppose you're right. I studied some of his theorems back in university and they're still more complicated than anything I've seen since. It's really too bad you didn't inherit some of his abilities, although, I suppose it wouldn't really work that way in your case. Well, if nothing else, thank you for stopping by and providing the latest batch of virus samples. I really wish I could give you some indication of any progress but with this last experiment showing no signs of success, I just can't say when that will be."

The man smiled and held his hand up, motioning for her to stop. "Please, you don't have to do that. As long as you two keep working on this project, I'll be happy, progress or no."

She brought her hand to her forehead, trying to massage the ache that was slowly growing in her skull. "Right. The two of us. I haven't been able to talk about this to anyone, but he's been getting worse lately. He keeps watching the reports on how the war is going. The way he talks you'd think there were killings outside our doorstep. On one hand, I know where he's coming from and I can even sympathize with him. After all, he did have family in the last city to be hit by an attack. Still, I can't allow his negative sentiments to get in the way of our work. We have to maintain our objectivity and keep on working until we've exhausted every last possible combination."

The man slowly nodded his head. "I understand. There's enough bad sentiment going around that that really doesn't surprise me. It hasn't become a major problem, has it?"

"No, it hasn't affected our work. I just wish he'd let me in on this secret project he has on the side. Something has got him very excited, and I'd love to see what it is. But forcing it out of him will probably just make him withdraw further into his laboratory and that's the last thing I need. Like it or not, we need him on this. He's the best programmer I've ever seen and his designs on robot structure are incredible. If only his personal feelings weren't so… Oh, Guntram! When did you get here?"

The young man turned to look and saw an older man, of average height and surly disposition, standing in the doorway behind him. "Just now. I was coming to give you some new information I uncovered, but I didn't realize that 'he' would be here. Sorry for the intrusion, I'll go."

However, his tone of voice indicated that he was anything but sorry, and so the woman stood. "Guntram! Please be courteous."

The young man stood quickly. "That's alright doctor. I don't want to cause any strife between the two of you. I'll go. Let me know of any progress you make." At this point, the young man walked out smiling briefly at the older doctor, but getting nothing in return.

After a few seconds, the woman began angrily ranting. "Guntram, I can not believe your behavior. That man is the only thing that's been keeping us funded for the past year and a half, he's reason we've been able to make as much progress as we have."

Guntram lowered his eyes and spoke through gritted teeth. "He's also the reason I fear for my daughter's life every time I hear about another attack on the news. If he had never existed the world would be better off. And for the last time Alexis, don't call him a man! It's insulting to even compare his kind with ours."

"You can't blame him for it! None of it was his choice in the first place! He didn't ask to be built, and he wasn't the one who started the mass-production."

"He was an old man's last mistake. A mistake that has cost the world millions of lives. The only thing they're good for is killing each other off."

Outside the office, the young man continued on his way out of the building. He didn't want to eavesdrop, but with his ears, it was hard not to hear what was being said about him. He was glad that Alexis was standing up for him and his kind, it made him feel he had a reason to live. However, he knew that Guntram's views were in the majority. For all it's progress, mankind had not gotten used to sharing it's planet with another sapient race and had remained cautious of it's new neighbors at best . He could understand the hostility towards his people; it was true that the wars of this era were worse by far than anything the last century produced. The Eurasia incident in particular had nearly wiped out humanity, closer to extinction than even the Cold War of the twentieth century had put it. And through it all, he did feel guilt, tremendous guilt. After all, in a way, they were all his children even if it didn't feel that way. Their sins reflected on him and he did all he could to redeem them.

He sighed as he heard the doctors grow silent. He was glad they had stopped fighting; they were the best chance he had of finally putting an end to the problem he had been fighting for decades and he needed them to cooperate with each other. He thought of all the friends he had lost in one way or another over the years. Most of them were dead, one had gone to the stars, and his best friend had been missing for years. He was doing this for them. He thought of his father's last wish, a unity between humans and his kind. He was doing this for him. Finally he stopped and thought of the future, a time that had yet to be written, a place that he had named Elysium. He was doing it for that. Most of all though, he was doing it because that's who he was.

Resolve strengthened, Mega Man X walked out the door towards a future that was looking brighter every moment.

It was the calm before the storm.

* * *

End Prologue


	2. Chapter 1 Current Affairs

_"On to the issue of the current developments in the ongoing Maverick Wars: with the rebuilding, and restructuring, of Maverick Hunter Headquarters, along with Sigma's termination at the Battle of Old Tokyo, there has been a marked decrease in maverick activity. This coupled with the declaration of Maverick Hunter X, the new leader of the Maverick Hunters, that all maverick activity would be curtailed within the next two years has given many around the world a new sense of security they haven't felt since the days before the Eurasia crash." -International News Network_

Chapter 1 - Current Affairs

X enjoyed his long walks through the ruins of Old Tokyo. They gave him a chance to be away from the havoc that was his life, even if only for a couple of hours. Even the calm of the desolate landscape didn't help however, when he heard the news of another hit and run attack by the mavericks on another city. Frustration at not being able to prevent the attacks was his immediate reaction, which was further magnified as the casualty reports came in. Not a single maverick casualty; the hunters had arrived in time to help with the clean up and medical evac of the wounded, but there were dozens of dead for every one they saved. Though by all appearances, X was a young adult, it was times like this when he felt every one of his many decades of existence weighing down upon him. It was times like this that he went on his walks, and reminisced, always making sure to keep his comm channel open should some emergency arise.

For a long time now, the Maverick Hunters have been rebuilding their organization, trying to recreate the infrastructure that existed before the catastrophe that claimed the lives of nearly every hunter unit and hundreds of civilian hunters. It had also cost him nearly all of his best friends; Lifesaver, Douglas, Layer, Pallette, Signas, Axl, even Vile through some twist of fate, and… Even now, years and years after it had happened, the memory caused him pain. 'And Alia…'

He loved her, in the only way two artificial life forms could. Had they been human, X had no doubt that they would have married. Such a simple fantasy, and how he envied humans for being able to express their love in so many unique ways. They had shared one last kiss, right before her systems shut down and she, for lack of a better word, 'died.' He had hoped that she might be recovered from the collapsed wreckage of Maverick Hunter Headquarters, but her control chip, a robot's soul if it could be called that, had been snapped during the building's collapse. The woman he loved was gone, and he, somewhat reluctantly, let her body be taken to a recycling factory, where hopefully she would help make more reploids. 'A kind of rebirth,' X mused, interested by the philosophical implications.

It was after a few hours that he came across a makeshift shrine in the open wasteland that was Old Tokyo. On it were inscribed the words, 'Here lie Maverick Hunters, the victims of the last Sigma uprising. They fought with honor and courage and in the end, all were redeemed.' X had added that last line in regards to one particular hunter. Nearly every single hunter had been taken to recycling centers, much the same way Alia had been, but there was one hunter here that X had personally buried with full honors.

The reploid Vile had, for decades, been a fairly persistent thorn in the hunter's collective side. Even before Sigma's first uprising, Vile had been a dangerously unstable maverick hunter, taking down mavericks with brutal force and no care for the significant collateral damage he caused along the way. However, he also possessed a talent for tactical thinking, which was one of the reasons Sigma released him during the first Uprising. Vile's most defining characteristic though, was his intense hatred for Mega Man X, which ultimately stemmed from his belief that X was undeserving of the many benefits he received.

After several deaths and subsequent re-activations, everything changed. Vile managed to get close to X and began to reappraise X's character. Vile soon came to realize that this was not the same simpering reploid he had known so many years ago. X had grown to fully understand what being a hunter entailed and had become what he himself had strove for when he had been a hunter. He came to realize that his vendetta had been because of a grievous misunderstanding as he realized how wrong he had been, both about X and himself. Through some extraordinary circumstances, he and X reconciled their pasts, and fought one last battle together. In the end, Vile managed to buy X the time he needed to prepare for Zero's attack by sacrificing himself in combat, being destroyed for the final time.

X sighed. He knew there was no way to recover Vile, his control chip had been destroyed during the fight with Zero, and because Vile had been considered an enemy for decades his remains would not be used to create new reploids. Humans were very paranoid about using the parts of former mavericks and X knew that anything he said would be ignored; even he wasn't that influential. So, much as it pained him, X stayed silent about Vile, choosing instead to honor him with a simple burial and a message that he knew Vile would have understood. "After so much fighting, I only really knew you for a few minutes, but I wouldn't have traded those for anything. Rest easy friend. I never got to say how much I appreciated what you did for me, so I hope this makes up for it."

The comm unit in X's helmet chimed. X let out a small sigh and activated it. "X here."

"Commander, we've just received word of a maverick attack. We're sending you the coordinates now."

X was all business now, he had to quickly take decisive action to minimize the damage that he knew was sure to come. "Good work, I'll be en route shortly. Have the fourth squad assemble and beam to my location as soon as possible. X out." And in a flash of light, X was gone.

Minutes later X rematerialized in the middle of a commercial zone. Doing a quick survey of the surroundings, he saw a multi-story office building on fire. He charged ahead, trying his best to get through the crowd of people that were running out of the building's entrance. Luckily, he was well known among the populace so he had no trouble getting past the armed humans that were doing their best to evacuate the remaining civilians. X dashed into the building and began looking for any signs of the maverick, or mavericks, that caused all this destruction.

The sound of the blazing fire slowly destroying the surrounding area would have all but overwhelmed a human. It was so loud that X almost missed the sound of a charging buster behind him. Trusting instincts honed by decades of combat, he quickly knelt down and rolled to one side as a large blue ball of super heated plasma soared through the spot his head had occupied an instant earlier. He quickly spun around and fired three shots towards where he judged the shot originated from. He smirked to himself, knowing how lucky he was; the maverick was still here. The smoke and the fire helped obscure the maverick from X, but it went both ways and X knew how to make his surroundings work for him. X closed his eyes and slipped into the smoke, vanishing from sight.

The maverick looked around the corner it had taken refuge behind, cursing his poor luck at botching his attack. He realized he should have been more careful when he saw who had come barging in to take him down, but he couldn't pass up the opportunity to take down one of his greatest enemies. The virus demanded violence and he had to satiate it. Now however, X had been alerted to his presence and he knew that he was outclassed. More maverick hunters were undoubtedly on their way and the Maverick Hunter Headquarters were probably already tracking all teleportation signals from the area. It would be best if he was able to silently exit the scene and get away on foot. Making his way to the closest window he entered an employee break room, and began to hear a whining noise. Looking around he saw that someone had left a pot of boiling water on the small stove, apparently for tea or some other beverage. The maverick scoffed at the idea and snuck towards the window.

Before the maverick knew what hit him, a sphere of super-powered energy of the brightest blue from directly above sent him reeling to the ground. He tried to get up but something very heavy landed on him with enough force to collapse the floor he was laying on. The structure gave way and he landed on the floor below, his internal energy readings warning him against taking any more damage. "Funny how trying too hard to be stealthy usually works against us, isn't it?" The maverick craned his neck to get a look at the one who addressed him.

Mega Man X stood on the maverick's back along with a fully charged buster that was aimed directly at his head. "I admit, it's been a long time since anyone has hid from me as well as you did. You should have just ran, you might have had a chance to escape. As it stands, do you have any last words?"

The maverick felt rage welling up in him, but managed to put it down as he spoke. "You can destroy me, but death is all that awaits you too. You have no idea what's coming do you X? You think the mavericks beaten, ha! You won't believe what we have planned for you and your precious humans." The maverick began to laugh.

X, not phased by the outburst, merely said, "I've seen the worst Sigma had to give. I'll take my chances." X fired, and the super shot tore through the maverick. X braced himself as the explosion from the maverick's power core overloading washed over him. The fire died down, leaving X covered in soot as he waked over to the remains.

There was another crash behind him and X quickly spun around, readying his buster. "Identify yourself!"

A voice came from near the entrance of the building. "Sir! Lieutenant Emery of the Fourth reporting for backup."

X lowered his buster, canceling the charge he had been building. "Looks like you're a little late Em. There was only one and I already dispatched him. If you and your men want to go out and help with the damage control I'll get the samples I need from this thing." X had become a lot less formal now that the situation had been diffused. One of the maverick hunters approached with a containment unit, which X took and prepped for use. X walked over and removed the cover of the maverick's control chip. Taking the chip in his hands, he saw a small black spark shoot between the chip and his hand. Sighing, X put the chip in the containment unit, sealed it, and walked out. "Emery, I've got the sample, I'll be taking this for examination. You and your men should be able to deal with the clean up."

Emery stood at attention, "roger that sir. You all right?"

It was a question that X had heard over a dozen times already. The other hunters were always concerned whenever X handled maverick remains. The Virus was tenacious and would attempt to infect any reploid that came into contact with it, including X. Fortunately, X had discovered how to self-delete the virus, providing him with an invaluable immunity to reinfection. The black spark had been the virus' attempt at survival, but the second it had happened, X fought it off. Still, despite X's track record in regards to fighting off the virus, his men always asked if he was alright. It made X smile as he replied. "Yes, I'm doing just fine. Now I need to get back to headquarters."

Emery saluted. "Yes sir. We'll handle it from here."

X nodded and disappeared in a bright blue beam of light.

After about a minute of transfer, X rematerialized inside the transporter room of the New Maverick Hunter Headquarters. On the other side of the room, an operator was overseeing the transporter signatures of everything that beamed into the headquarters. As X rematerialized, a silent countdown appeared on the operator's console. The operator looked to X, who held up the sealed container that he had stored the virus sample in. X said, "it's alright, I imagine it's picking this up."

The operator nodded and entered the code to deactivate the countdown. "Got lucky did we sir? I haven't seen you return from a hunt with one of those for over a month now."

X nodded. "Very lucky. The maverick was still there and he tried to fight me."

The operator let out a whistle. "I'm sure he regretted that right before you scrapped him. Well anyways, I'm glad to hear the good news, unfortunately, there is some news that I imagine you'll not be too keen on. We just got a call from the GDC, and they want to talk to you."

X's smile vanished as a look of concern crossed his face. "I see. Well, I suppose it'd be bad form for me to keep them waiting. Can you see that this sample is documented and sent to Dr. du Blanc for research?"

"I certainly can sir. Good luck with the meeting."

X let out a small sigh. "Thanks, I hope I don't need it.

Even though his rank as acting supreme commander of the Maverick Hunters had been merely a field promotion, X retained the position almost purely on the basis that he was the most senior maverick hunter on the planet. Combine that with the fact that he was also the precursor to every other reploid, and indeed, it seemed an insane idea that he should not be the head of the Hunters. Of course, his other qualifications didn't hinder him, what with him being the sole survivor of every single maverick uprising and his status as one of the greatest hunters firmly established. His talents as an orator while acting as main liaison between the world's governments and the Maverick Hunters also made him more than apt to act as the head of an organization that was consistently under scrutiny from the human run governments; he was very good at cooling down potentially volatile situations.

Now, he had to make sure those speaking skills were still sharp. "Members of the Global Defense Council, I received word that you wanted to meet with me?"

"Yes, thank you for agreeing to talk to us on such a short notice Commander X. We are all aware of the work you do and are loath to interrupt it." The speaker was an Englishman by the name of Kent Auter, a former Prime Minster who, for all his politeness, had a history of passing legislation that hampered the movement for equal rights for reploids. He would only be an asset to X if he knew that it would benefit his own interests. "We have called you here to report on the status of your current actions regarding the clean up of the remaining maverick forces."

X let out a small sigh, one that would not be noticed by the council members. "Yes sir. I've sent the council the latest updates in my last report. I assume that's what you want to talk to me about?"

Councilman Auter grinned a bit. "Yes, indeed. We're concerned with how long your supposed 'cleaning action' is taking. In your preliminary report, you stated that maverick activity would be put down within two to three years. Commander, how do you explain the fact that your predicted results are now well over a decade overdue? Is there some sort of problem with the way the Maverick Hunters are operating?"

X had to calm himself as he thought about how to best organize his response. The implied accusation, that the Maverick Hunters were of no use, stung X like nothing else could. All of the friends that died as a result of Maverick trickery flashed through X's memory. The thought that they all had died in vain had been something that X had contended with before, but now he put that out of his head as he prepared to speak. "Councilman Auter, members of the GDC, I acknowledge that my prediction has been invalidated but rest assured, it is no one's fault but the mavericks. All of our data about the way they operate was rendered useless once Sigma and his generals were destroyed at the Ruins of Old Tokyo. The new hit-and-run tactics they've been employing have rendered our normal operating strategy next to worthless. Overall, however, maverick activity has been at a record decline. We are stopping them, it's just a matter of time."

"Time that could be well spent working on other things Commander. Your war of attrition with the mavericks is taking time and funds away from vital projects. There are still portions of the Earth that have not recovered from the events of the Eurasia colony crash. Not to mention the disaster of the Jakob Orbital Elevator and what happened with the copy reploid Lumine."

"With all due respect sir, the GDC read the report on the copy reploids, but failed to initiate any sort of standing provisions for the halt in production of copy chips, nor for the seizure of the copy chips already installed in new-generation reploids." Councilman Auter had struck a nerve. X remembered his friend Axl who had had his body taken over by Lumine's personality data and who had only freed himself through an act of suicide. "Now that the production of copy-chips with data from Sigma has continued unabated for years, the Maverick Hunters cannot legitimately be blamed for the situation that has presented itself."

Auter looked miffed. "A valid point Commander. Regardless of who or what is to blame, this struggle is taking its toll on everyone. I'm asking you now Commander, what can be done to better facilitate the results we all want?"

X decided that now was a good time to play the ace he had been hiding. "Well sir, I have already created a privately funded initiative to uncover a cure for the Maverick Virus."

There were surprised murmurs from some of the other councilmen as Auter let a look of shock briefly come over him. "A privately funded initiative? When did you start this?"

X put as much confidence in his voice as he could. Despite the fact that he had hidden this from the GDC, the scientists had yet to make any headway to solving the problem of the Maverick Virus. "Nine months ago. Since then the team has made significant head way in analyzing the programming of the Maverick Virus and coming up with a conclusive cure for it."

The murmurs turned into full out conversations between the other members of the council. X could tell that many council members were pleased to hear of this turn of events. Auter looked around and could see that X currently had the public support and began to speak. "Well Commander, I must say this is a surprising revelation, and your initiative in founding this project is commendable. Although we frown upon secret projects such as this, I am sure the other members of the GDC are willing to respect the domain of your responsibilities. If that is all, then I believe I can call this meeting adjourned. Once again, we thank you for your time and wish you and your forces success Commander." Auter rose from his podium and made his way out of the council chambers.

X knew that Auter hadn't appreciated that, but there was little the human could do at the moment. With so much support from the members of the council, X guessed it would be months before he would be called in for questioning again. Months that would give him and the Maverick Hunters more time to collect samples of virus data from mavericks for the doctors to examine. Still, X understood that if the same amount of progress was made over the next few months, Auter would no doubt attempt payback for being shown up by X. X had to get results and fast.

He had no clue how soon he would have them.

* * *

End Chapter 1

A/N: After a very long hiatus (writer's block) I update with another chapter. As usual please read, enjoy, and leave some feedback, I love hearing from people.


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